| Partitioning and combining data in phylogenetic analysis JJ Bull, JP Huelsenbeck, CW Cunningham, DL Swofford, PJ Waddell Systematic Biology 42 (3), 384-397, 1993 | 1143 | 1993 |
| Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods DL Swofford, PJ Waddell, JP Huelsenbeck, PG Foster, PO Lewis, ... Systematic biology 50 (4), 525-539, 2001 | 480 | 2001 |
| Potential mechanisms for cancer resistance in elephants and comparative cellular response to DNA damage in humans LM Abegglen, AF Caulin, A Chan, K Lee, R Robinson, MS Campbell, ... Jama 314 (17), 1850-1860, 2015 | 476 | 2015 |
| Molecular systematics DL Swofford, GJ Olsen, PJ Waddell, DM Hillis, C Moritz, BK Mable | 474 | 1996 |
| Towards resolving the interordinal relationships of placental mammals PJ Waddell, N Okada, M Hasegawa Systematic Biology 48 (1), 1-5, 1999 | 420 | 1999 |
| A phylogenetic foundation for comparative mammalian genomics PJ Waddell, H Kishino, R Ota Genome Informatics 12, 141-154, 2001 | 332 | 2001 |
| Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA J Adachi, PJ Waddell, W Martin, M Hasegawa Journal of molecular evolution 50, 348-358, 2000 | 274 | 2000 |
| Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders Y Cao, A Janke, PJ Waddell, M Westerman, O Takenaka, S Murata, ... Journal of Molecular Evolution 47, 307-322, 1998 | 270 | 1998 |
| Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. PJ Lockhart, AW Larkum, M Steel, PJ Waddell, D Penny Proceedings of the National Academy of Sciences 93 (5), 1930-1934, 1996 | 257 | 1996 |
| General time-reversible distances with unequal rates across sites: mixing Γ and inverse Gaussian distributions with invariant sites PJ Waddell, MA Steel Molecular phylogenetics and evolution 8 (3), 398-414, 1997 | 254 | 1997 |
| Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome JS Rest, JC Ast, CC Austin, PJ Waddell, EA Tibbetts, JM Hay, DP Mindell Molecular phylogenetics and evolution 29 (2), 289-297, 2003 | 221 | 2003 |
| Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with … PJ Waddell, Y Cao, J Hauf, M Hasegawa Systematic Biology 48 (1), 31-53, 1999 | 181 | 1999 |
| Widespread introgression across a phylogeny of 155 Drosophila genomes A Suvorov, BY Kim, J Wang, EE Armstrong, D Peede, ERR D’agostino, ... Current Biology 32 (1), 111-123. e5, 2022 | 164 | 2022 |
| Correspondence analysis of genes and tissue types and finding genetic links from microarray data H Kishino, PJ Waddell Genome Informatics 11, 83-95, 2000 | 161 | 2000 |
| Evolutionary trees of apes and humans from DNA sequences P Waddell Handbook of human symbolic evolution, 53-73, 1996 | 151 | 1996 |
| Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models PJ Waddell, S Shelley Molecular phylogenetics and evolution 28 (2), 197-224, 2003 | 149 | 2003 |
| Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework PJ Waddell, Y Cao, M Hasegawa, DP Mindell Systematic Biology 48 (1), 119-137, 1999 | 141 | 1999 |
| The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Y Cao, PJ Waddell, N Okada, M Hasegawa Molecular biology and evolution 15 (12), 1637-1646, 1998 | 123 | 1998 |
| Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters R Ota, PJ Waddell, M Hasegawa, H Shimodaira, H Kishino Molecular biology and evolution 17 (5), 798-803, 2000 | 118 | 2000 |
| Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. D Penny, M Steel, PJ Waddell, MD Hendy Molecular biology and evolution 12 (5), 863-882, 1995 | 117 | 1995 |
